rs6465657

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014916(LMTK2):c.998+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152012 control chromosomes in the gnomAD Genomes database, including 13407 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 13407 hom., cov: 33)

Exomes 𝑓: 0.41 ( 23378 hom. )

Consequence

LMTK2
NM_014916 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.617

Links

LMTK2 (HGNC:17880):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMTK2	NM_014916.4 linkuse as main transcript	c.998+17C>T		intron_variant		ENST00000297293.6
LMTK2	XM_011515981.4 linkuse as main transcript	c.992+17C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMTK2	ENST00000297293.6 linkuse as main transcript	c.998+17C>T		intron_variant		1	NM_014916.4	P1

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56662

AN:

152012

Hom.:

13407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.430

GnomAD3 exomes

AF:

0.405

AC:

96530

AN:

238114

Hom.:

23378

AF XY:

0.415

AC XY:

53363

AN XY:

128538

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.593

Gnomad EAS exome

AF:

0.139

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.472

Gnomad NFE exome

AF:

0.545

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.487

AC:

703442

AN:

1444152

Hom.:

183305

AF XY:

0.483

AC XY:

346528

AN XY:

717764

show subpopulations

Gnomad4 AFR exome

AF:

0.0969

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.587

Gnomad4 EAS exome

AF:

0.120

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.479

Gnomad4 NFE exome

AF:

0.537

Gnomad4 OTH exome

AF:

0.473

Alfa

AF:

0.510

Hom.:

48571

Bravo

AF:

0.360

Asia WGS

AF:

0.179

AC:

623

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

2.9

Dann

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over